X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2Ffeatures%2Fpdbviewer.html;h=8deebaeab2621d423ca0ff47892a565700126037;hb=4884e25f5b34c098cbfe5f207b2a3d938c9b82c4;hp=97471a2e9899777db4c7c60ab162e9cf3d2dab82;hpb=bb105fcca41253815982584f4c8f6fae1f8e10a3;p=jalview.git diff --git a/help/html/features/pdbviewer.html b/help/html/features/pdbviewer.html index 97471a2..8deebae 100755 --- a/help/html/features/pdbviewer.html +++ b/help/html/features/pdbviewer.html @@ -1,14 +1,43 @@ + PDB Viewer +

The Jalview internal PDB Viewer
+Since Jalview 2.3, the Jmol PDB Viewer is +the main method for viewing PDB +structures. The documentation below concerns the original Jalview +PDB viewer, which is only used in situations where Jmol is unavailable +or cannot operate.

The PDB Viewer Window

This interactive structure viewing window is opened by selecting -the "Sequence→View PDB entry:" entry in -the sequence id pop-up menu. This -can only be done for sequences which have an associated -PDB structure.

+entries from the "Structure→" submenu + of the sequence + id pop-up menu. The internal PDB viewer is not able to show + superpositions, so no other options are provided. Structures can only + be viewed for sequences which have an associated +PDB structure, and the PDB Viewer will only be associated with the +particular alignment view from which it was opened.

Controls

The structure is rendered as an alpha-carbon trace. Moving the mouse over the structure brings up tooltips with a residue name and PDB @@ -121,9 +150,9 @@ and alpha carbon location.

  • Show All Chains
     When turned on, shows all chains in the PDB file, not just the one associated with a sequence in the alignment window.
    • -
  • Associate View
    +